I believe the problem you are seeing is stemming from the fact that in Windows 8.1 the DNS Client began sending IPv4 & IPv6 queries in parallel. Where as in previous OS's the IPv4 query was sent and then the IPv6 query was serialized.

So what I believe is happening is that the IPv6 query is hitting your ISP first and responding in such a way as to make the DNS Client think the name is unresolvable.

Other replies to this thread support this since they indicate that disabling IPv6 makes the name resolution work the way you need it too. So another way to fix this would be to revert the DNS Client behavior to be like it used to be, you can accomplish that
by setting this registry key:

I believe the problem you are seeing is stemming from the fact that in Windows 8.1 the DNS Client began sending IPv4 & IPv6 queries in parallel. Where as in previous OS's the IPv4 query was sent and then the IPv6 query was serialized.

It was also working on Win 7 and 8 and 8.1 ... so if only Win 8.1 hat this feature it is not the real problem.

Ok, since this seems to be a split tunnel issue. Do you notice any difference when using fully qualified domain names as opposed to short names? Also take a look at ipconfig /all and see if the VPN interface has DNS suffixes configured for it that correspond
to the domain names reachable only over the VPN. Lastly, have you taken a look at the routing metrics for the VPN interface vs your LAN\ISP? The DNS client uses this to determine the interface to use if the interfaces are missing any suffix configuration.